Three-dimensional structure of the 3′X-tail of hepatitis C virus RNA in monomeric and dimeric states

Cantero-Camacho A, Fan L, Wang Y, Gallego J, RNA 2017 Jun 19 :rna.060632.117 DOI

SASDBM7 – Subdomain SL1 of hepatitis C virus RNA domain 3'X at low ionic strength

Subdomain SL1 of hepatitis C virus
MWexperimental 15.2 kDa
MWexpected 15 kDa
log I(s) 5.80×10-2 5.80×10-3 5.80×10-4 5.80×10-5
Subdomain SL1 of hepatitis C virus small angle scattering data  s, nm-1
ln I(s)
Subdomain SL1 of hepatitis C virus Guinier plot ln 5.80×10-2 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
Subdomain SL1 of hepatitis C virus Kratky plot 1.104 0 3 sRg
p(r)
Subdomain SL1 of hepatitis C virus pair distance distribution function Rg: 2.3 nm 0 Dmax: 8.1 nm

Experimental data validation


Fits and models


log I(s)
 s, nm-1
Subdomain SL1 of hepatitis C virus DAMMIN model
Synchrotron SAXS data from solutions of Subdomain SL1 of hepatitis C virus RNA domain 3'X at low ionic strength in 10mM Tris 0.1 mM EDTA, pH 7, were collected on the 12ID-B SAXS/WAXS camera on the storage ring Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.0886 nm (I(s) vs s, where s = 4π sin θ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 2 mg/ml were measured at 27°C. 30 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for RNA concentration. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

Subdomain SL1 of hepatitis C virus (SL1)
Mol. type   RNA
Organism   Hepatitis C virus
Olig. state   Monomer
Mon. MW   14.9 kDa
Sequence   FASTA